So I bottled two batches today.......Dang I hate to wash and sany bottles.....
Anyway my Pete's Wicked was a dry hop beer and I did it in secondary with hop pellets....

I made the mistake of direct dry hopping with pellets. So the pellet material was mostly on top and in cake....However some still in beer.

I heard no problems just use the auto syphon and it'll keep it out. I looked at it and said no way. I heard also about panty hose on tip so I wen that route. I got 4 gallons out but once I got to the last gallon it choked and I couldn't get it started again.

Also noticed the pellet material had got kicked up so it was all over the last gallon so I did the un thinkable and let it go..........

I got 1 and 3/4 of a case instead of my classic 2 cases with some to spare but damn it smelled and tasted good so I'm gonna have to go with acceptable loss.

Now the question is what should I do in future? I'm thinking a hop bag but will this allow the beer to get all the benefit of a dry hop?

You can use whole hops, which are superior for dry hopping in two ways. They (mostly) float, and they have all the aroma oils still intact. But if you can't get them, then pellets in a bag will work as fine as pellets can work.

I use a hop sock for all dry hopping, heck for ALL hopping period. Boil the sock for 10 or 15 min to sanitze it, drop the pellets in, tie it and drop it into secondary. I did an IPA a few weeks ago where I dry hopped with whole leaf hops. I was told by my LHBS that I didn't need a bag with whole leaf hops. Huge mistake in NOT using a hop sock or panty hose. Like you, I lost a lot of beer by not being able to get around all of the leaves. They expand, by the way! The beer is incredible. One of the best I have ever made, so I will do it again. But next time I will use something to contain the leaves.

If you use the "Bottling Bucket) can't you just auto-siphon it off normally then let it settle again and just bottle away?

From what I remember of my bucket it was never really good at getting all the beer on the bottom to begin with.

As for kegging with the dry-hopped pellets...I just say "Fug It" and write that first glass off to sediment.
(And since I only clean the lines every 4 kegs, it usually is tossed anyway as it blows out the last bits of the older beer)

I prefer whole hops for just about everything in brewing, especially dry hopping. I just throw my Dry Hops in loose then when it comes time to bottle I sanitze the biggest spoon I have and scoop out as much as possible. Then the little bit that is left over gets filtered out by the Bottle Filler. Takes a little extra time, but I like knowing that as much as possible of the Dry Hops is touching the beer. And the loss is minimal, maybe 1 beer's worth.

The first time I used pellets and a nylon hop bag, results were mostly good but the bag closed with a little tie-string which could not keep some of the pellets from finding their way out of the bag and into the beer. Another time I just threw them in there sans bag after someone had told me they would all sink to the bottom after a week and I could auto-siphon around them. That just wasn't true, they didn't sink and the auto-siphon did not keep them from ending up in my bottling bucket.

I've yet to try whole-flower hops but I'd have to either order those online or go pick them up at the store whereas I have pellets in my freezer. Has anyone come to an absolute conclusion on the best method?

I have yet to ever dry hop, so I don't know if this is out of the question, but if you are having trouble with the hop bag getting in the way, why not string it up? Tie a string to the bag and then to the outside of the bucket (handle perhaps) and the hops will be suspended in the beer and wont interfere at the bottom of the bottling bucket, or you could simply pull out the bag coming bottling.

I regularly DH big amounts of pellet hops in primary. I never get hop particles. I always cold crash my beer for a good 3-5 days before racking to keg or bottling bucket. No issues. I used to have issues but not that I cold crash everytime with that method, no more issues.